FMO DATABASE

FMODB ID: ZY84N

Calculation Name: 2XG8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XG8

Chain ID: D

ChEMBL ID:

UniProt ID: P0A3F4

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-577279.591681
FMO2-HF: Nuclear repulsion	541441.258284
FMO2-HF: Total energy	-35838.333397
FMO2-MP2: Total energy	-35944.072013

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(D:3:SER)

Summations of interaction energy for fragment #1(D:3:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-3.424	-1.048	0.017	-1.278	-1.115	0.002

Interaction energy analysis for fragmet #1(D:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.003

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	D	5	ASN	0	0.013	0.000	3.438	-3.962	-1.617	0.018	-1.251	-1.112	0.002
4	D	6	TYR	0	-0.066	-0.069	6.132	0.381	0.381	0.000	0.000	0.000	0.000
5	D	7	LEU	0	0.010	-0.001	9.793	0.190	0.190	0.000	0.000	0.000	0.000
6	D	8	ASN	0	-0.004	0.002	12.737	0.054	0.054	0.000	0.000	0.000	0.000
7	D	9	HIS	0	0.031	0.010	16.480	0.060	0.060	0.000	0.000	0.000	0.000
8	D	10	PRO	0	-0.007	-0.014	18.574	0.016	0.016	0.000	0.000	0.000	0.000
9	D	11	THR	0	-0.029	0.001	22.157	0.032	0.032	0.000	0.000	0.000	0.000
10	D	12	PHE	0	-0.025	-0.028	19.682	0.022	0.022	0.000	0.000	0.000	0.000
11	D	13	GLY	0	0.048	0.038	19.462	-0.036	-0.036	0.000	0.000	0.000	0.000
12	D	14	LEU	0	0.008	0.021	13.299	-0.047	-0.047	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.038	-0.024	12.695	0.061	0.061	0.000	0.000	0.000	0.000
14	D	16	TYR	0	0.016	-0.004	9.258	-0.054	-0.054	0.000	0.000	0.000	0.000
15	D	17	GLN	0	0.022	0.010	4.129	-1.264	-1.233	-0.001	-0.027	-0.003	0.000
16	D	18	ILE	0	-0.064	-0.019	6.811	-0.334	-0.334	0.000	0.000	0.000	0.000
17	D	19	CYS	0	-0.028	-0.031	6.507	0.094	0.094	0.000	0.000	0.000	0.000
18	D	20	SER	0	0.000	-0.013	7.222	-0.034	-0.034	0.000	0.000	0.000	0.000
19	D	21	PHE	0	-0.091	-0.041	8.846	0.147	0.147	0.000	0.000	0.000	0.000
20	D	22	GLY	0	0.024	0.002	11.499	-0.027	-0.027	0.000	0.000	0.000	0.000
21	D	23	ASP	-1	-0.948	-0.953	12.079	0.172	0.172	0.000	0.000	0.000	0.000
22	D	24	SER	0	0.015	-0.002	13.084	0.002	0.002	0.000	0.000	0.000	0.000
23	D	25	LYS	1	0.881	0.934	12.929	0.313	0.313	0.000	0.000	0.000	0.000
24	D	26	GLU	-1	-0.841	-0.914	8.358	-0.831	-0.831	0.000	0.000	0.000	0.000
25	D	27	LEU	0	-0.051	-0.004	9.992	0.102	0.102	0.000	0.000	0.000	0.000
26	D	28	PHE	0	0.025	-0.004	8.407	-0.349	-0.349	0.000	0.000	0.000	0.000
27	D	29	ALA	0	-0.008	-0.004	11.651	0.286	0.286	0.000	0.000	0.000	0.000
28	D	30	THR	0	-0.013	-0.015	13.689	-0.124	-0.124	0.000	0.000	0.000	0.000
29	D	31	LEU	0	0.007	0.001	12.694	0.027	0.027	0.000	0.000	0.000	0.000
30	D	32	TYR	0	0.027	0.016	15.908	0.056	0.056	0.000	0.000	0.000	0.000
31	D	33	ALA	0	0.042	0.038	19.460	0.073	0.073	0.000	0.000	0.000	0.000
32	D	34	GLN	0	-0.046	-0.019	19.359	-0.108	-0.108	0.000	0.000	0.000	0.000
33	D	35	ARG	1	0.939	0.958	15.865	0.851	0.851	0.000	0.000	0.000	0.000
34	D	36	LEU	0	-0.064	-0.008	18.814	0.057	0.057	0.000	0.000	0.000	0.000
35	D	37	PHE	0	0.009	-0.006	14.743	-0.078	-0.078	0.000	0.000	0.000	0.000
36	D	38	PHE	0	0.010	-0.005	15.223	0.101	0.101	0.000	0.000	0.000	0.000
37	D	39	LEU	0	0.027	0.019	14.313	-0.130	-0.130	0.000	0.000	0.000	0.000
38	D	40	VAL	0	-0.015	-0.004	12.643	0.080	0.080	0.000	0.000	0.000	0.000
39	D	41	ALA	0	0.025	0.002	13.863	0.019	0.019	0.000	0.000	0.000	0.000
40	D	42	PHE	0	0.011	-0.002	11.247	0.009	0.009	0.000	0.000	0.000	0.000
41	D	43	ASP	-1	-0.784	-0.876	17.094	-0.332	-0.332	0.000	0.000	0.000	0.000
42	D	44	ALA	0	-0.001	-0.007	19.089	0.028	0.028	0.000	0.000	0.000	0.000
43	D	45	ARG	1	0.861	0.944	21.128	0.309	0.309	0.000	0.000	0.000	0.000
44	D	46	GLY	0	0.009	-0.034	21.823	0.016	0.016	0.000	0.000	0.000	0.000
45	D	47	THR	0	-0.070	-0.028	16.990	-0.051	-0.051	0.000	0.000	0.000	0.000
46	D	48	ARG	1	0.940	0.991	18.676	0.334	0.334	0.000	0.000	0.000	0.000
47	D	49	PHE	0	0.052	0.007	15.632	-0.073	-0.073	0.000	0.000	0.000	0.000
48	D	50	GLU	-1	-0.887	-0.926	18.472	-0.312	-0.312	0.000	0.000	0.000	0.000
49	D	51	PRO	0	-0.011	0.010	18.943	-0.049	-0.049	0.000	0.000	0.000	0.000
50	D	52	ILE	0	0.036	0.022	16.906	0.041	0.041	0.000	0.000	0.000	0.000
51	D	53	GLY	0	0.035	0.016	20.205	-0.033	-0.033	0.000	0.000	0.000	0.000
52	D	54	ARG	1	0.990	0.973	19.669	0.385	0.385	0.000	0.000	0.000	0.000
53	D	55	ASN	0	0.010	0.000	20.020	-0.016	-0.016	0.000	0.000	0.000	0.000
54	D	56	GLU	-1	-0.848	-0.915	20.129	-0.270	-0.270	0.000	0.000	0.000	0.000
55	D	57	ALA	0	0.033	0.018	16.136	0.011	0.011	0.000	0.000	0.000	0.000
56	D	58	ARG	1	0.909	0.948	16.464	0.216	0.216	0.000	0.000	0.000	0.000
57	D	59	MET	0	0.022	0.012	17.988	0.041	0.041	0.000	0.000	0.000	0.000
58	D	60	LEU	0	-0.013	-0.001	15.734	0.045	0.045	0.000	0.000	0.000	0.000
59	D	61	VAL	0	0.022	0.005	12.170	0.037	0.037	0.000	0.000	0.000	0.000
60	D	62	ASP	-1	-0.847	-0.912	14.396	-0.026	-0.026	0.000	0.000	0.000	0.000
61	D	63	ASN	0	-0.071	-0.053	17.127	0.103	0.103	0.000	0.000	0.000	0.000
62	D	64	ARG	1	0.984	1.013	9.586	-0.321	-0.321	0.000	0.000	0.000	0.000
63	D	65	LEU	0	0.009	-0.017	12.264	0.123	0.123	0.000	0.000	0.000	0.000
64	D	66	ARG	1	0.853	0.923	14.404	0.074	0.074	0.000	0.000	0.000	0.000
65	D	67	GLN	0	-0.038	-0.046	14.743	-0.001	-0.001	0.000	0.000	0.000	0.000
66	D	68	LEU	0	0.026	0.020	9.569	0.047	0.047	0.000	0.000	0.000	0.000
67	D	69	ARG	1	0.894	0.963	13.540	-0.457	-0.457	0.000	0.000	0.000	0.000
68	D	70	ARG	1	0.895	0.964	15.731	-0.221	-0.221	0.000	0.000	0.000	0.000
69	D	71	ASP	-1	-0.844	-0.918	13.249	0.894	0.894	0.000	0.000	0.000	0.000
70	D	72	ALA	0	-0.001	-0.005	15.502	0.043	0.043	0.000	0.000	0.000	0.000
71	D	73	SER	0	0.105	0.047	11.810	-0.001	-0.001	0.000	0.000	0.000	0.000
72	D	74	LEU	0	-0.023	0.009	10.551	0.090	0.090	0.000	0.000	0.000	0.000
73	D	75	GLN	0	-0.043	-0.043	12.774	-0.069	-0.069	0.000	0.000	0.000	0.000
74	D	76	GLU	-1	-0.935	-0.951	15.628	0.757	0.757	0.000	0.000	0.000	0.000
75	D	77	TYR	0	-0.006	0.011	11.660	0.052	0.052	0.000	0.000	0.000	0.000
76	D	78	ASN	0	0.005	-0.032	13.589	-0.006	-0.006	0.000	0.000	0.000	0.000
77	D	79	GLN	0	-0.024	-0.002	15.494	-0.054	-0.054	0.000	0.000	0.000	0.000
78	D	80	LEU	0	0.039	0.023	16.349	-0.056	-0.056	0.000	0.000	0.000	0.000
79	D	81	GLN	0	-0.012	-0.015	14.242	0.049	0.049	0.000	0.000	0.000	0.000
80	D	82	GLN	0	-0.080	-0.043	17.509	-0.065	-0.065	0.000	0.000	0.000	0.000
81	D	83	VAL	0	-0.001	0.010	20.536	-0.047	-0.047	0.000	0.000	0.000	0.000
82	D	84	PHE	0	0.025	0.015	19.775	-0.038	-0.038	0.000	0.000	0.000	0.000
83	D	85	LYS	1	0.971	0.967	21.733	-0.343	-0.343	0.000	0.000	0.000	0.000
84	D	86	GLN	0	-0.035	-0.031	23.661	-0.030	-0.030	0.000	0.000	0.000	0.000
85	D	87	THR	0	-0.004	0.009	24.780	-0.024	-0.024	0.000	0.000	0.000	0.000
86	D	88	PHE	0	-0.047	-0.007	23.006	-0.015	-0.015	0.000	0.000	0.000	0.000
87	D	89	LEU	0	-0.035	0.004	22.615	-0.036	-0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:3:SER)